scholarly journals Spatial Design of Polymicrobial Oral Biofilm in Its Native Disease State

2020 ◽  
Vol 99 (6) ◽  
pp. 597-603 ◽  
Author(s):  
D. Kim ◽  
H. Koo
Keyword(s):  
Spatial Organization ◽  
Disease Process ◽  
Genotypic Diversity ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
3 Dimensional ◽  
Spatial Design ◽  
Oral Biofilms ◽  
And Function ◽  
Human Infections

Biofilms are structured microbial communities adhered to surfaces that cause many human infections. The study of oral biofilms has revealed complex composition, spatial organization, and phenotypic/genotypic diversity of the resident microbiota at the various sites in the mouth. Yet, knowledge about the spatial arrangement, positioning, and function of the polymicrobial community across the intact biofilm architecture remains sparse. Using multiple length scale imaging and computational analysis, we discovered unique spatial designs comprising mixed interbacterial species and interkingdom communities within intact biofilms formed on teeth of toddlers with caries. Intriguing structural patterns ranging from intermixed communities with extensive coaggregation (including bacterial-fungal clustering) to spatially segregated species forming a multilayered architecture were found. Among them, a distinctive 3-dimensional structure exhibited densely clustered cariogenic pathogens that were surrounded by outer layers of mixed bacterial communities in juxtaposition, forming a highly ordered spatial organization. These findings are particularly relevant as we approach the postmicrobiome era whereby studying the spatial structure of the pathogen and commensal microbiota may be important for understanding the microbiome function at the infection site to coordinate the disease process in situ.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Three dimensional structure of the leishmania amastigote as revealed by computer-aided reconstruction from serial sections

Parasitology ◽  
1986 ◽  
Vol 92 (1) ◽  
pp. 13-23 ◽  
Author(s):  
G. H. Coombs ◽  
L. Tetley ◽  
V. A. Moss ◽  
K. Vickerman
Keyword(s):  
Cell Volume ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Leishmania Mexicana ◽  
Cell Organelles ◽  
3 Dimensional ◽  
Computer Aided ◽  
Total Cell Volume

SUMMARYComputer-aided reconstruction from serial sections has been used to analyse the 3-dimensional structure of entire amastigotes of Leishmania mexicana mexicana and to determine the number, arrangement and volume of each organelle. In two reconstructions, the lysosome-like ‘megasomes’ were the most numerous organelle, there being 34 in one amastigote, and they comprised as much as 15% of the total cell volume. In contrast, as few as 9 glycosomes were present, accounting for less than 1% of the cell volume. The unitary nature of the mitochondrion was confirmed and its complex basket-like structure was revealed. The spatial arrangement of the cell organelles is here displayed in stereo-pairs.

scholarly journals STORM imaging reveals the spatial arrangement of transition zone components and IFT particles at the ciliary base in Tetrahymena

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Khodor S. Hazime ◽  
Zhu Zhou ◽  
Ewa Joachimiak ◽  
Natalia A. Bulgakova ◽  
Dorota Wloga ◽  
...  
Keyword(s):  
Transition Zone ◽  
Spatial Organization ◽  
Intraflagellar Transport ◽  
Spatial Arrangement ◽  
Interaction Sites ◽  
Narrow Region ◽  
Cilia Formation ◽  
Axial Dimension ◽  
Optical Reconstruction ◽  
And Function

AbstractThe base of the cilium comprising the transition zone (TZ) and transition fibers (TF) acts as a selecting gate to regulate the intraflagellar transport (IFT)-dependent trafficking of proteins to and from cilia. Before entering the ciliary compartment, IFT complexes and transported cargoes accumulate at or near the base of the cilium. The spatial organization of IFT proteins at the cilia base is key for understanding cilia formation and function. Using stochastic optical reconstruction microscopy (STORM) and computational averaging, we show that seven TZ, nine IFT, three Bardet–Biedl syndrome (BBS), and one centrosomal protein, form 9-clustered rings at the cilium base of a ciliate Tetrahymena thermophila. In the axial dimension, analyzed TZ proteins localize to a narrow region of about 30 nm while IFT proteins dock approximately 80 nm proximal to TZ. Moreover, the IFT-A subcomplex is positioned peripheral to the IFT-B subcomplex and the investigated BBS proteins localize near the ciliary membrane. The positioning of the HA-tagged N- and C-termini of the selected proteins enabled the prediction of the spatial orientation of protein particles and likely cargo interaction sites. Based on the obtained data, we built a comprehensive 3D-model showing the arrangement of the investigated ciliary proteins.

scholarly journals Telomeres and Age-Related Diseases

Biomedicines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1335
Author(s):  
Hans-Jürgen Gruber ◽  
Maria Donatella Semeraro ◽  
Wilfried Renner ◽  
Markus Herrmann
Keyword(s):  
Telomere Length ◽  
Analytical Techniques ◽  
Telomerase Activity ◽  
Dimensional Structure ◽  
Protective Function ◽  
3 Dimensional ◽  
Age Related ◽  
Telomere Biology ◽  
Linear Chromosomes ◽  
And Function

Telomeres are at the non-coding ends of linear chromosomes. Through a complex 3-dimensional structure, they protect the coding DNA and ensure appropriate separation of chromosomes. Aging is characterized by a progressive shortening of telomeres, which compromises their structure and function. Because of their protective function for genomic DNA, telomeres appear to play an important role in the development and progression of many age-related diseases, such as cardiovascular disease (CVD), malignancies, dementia, and osteoporosis. Despite substantial evidence that links telomere length with these conditions, the nature of these observations remains insufficiently understood. Therefore, future studies should address the question of causality. Furthermore, analytical methods should be further improved with the aim to provide informative and comparable results. This review summarize the actual knowledge of telomere biology and the possible implications of telomere dysfunction for the development and progression of age-related diseases. Furthermore, we provide an overview of analytical techniques for the measurement of telomere length and telomerase activity.

‘Small House Spatiality: A Comparative Space Syntax Application’

2017 ◽  
Vol 42 (2) ◽  
pp. 58-67
Author(s):  
Ayça Arslan ◽  
Türkan Ulusu Uraz
Keyword(s):  
Open Space ◽  
Spatial Organization ◽  
Space Syntax ◽  
Spatial Relations ◽  
Spatial Arrangement ◽  
Spatial Design ◽  
Small House ◽  
Increasing Demand ◽  
Spatial Depth ◽  
House Design

It has recently come to light that there is an increasing demand for a new type of small house design, which vary in area from 20 square metres to 100 square metres and even more. Being remarkably different from traditional types of spatial organizations, the new house types present an open plan concept with a highly flexible and adaptable spatial arrangement that exhibit diverse functional spaces within one open, integrated space. In light of this, the main aim of this study is to reveal the new dynamics of spatial organization found in today's small house types and identify the significant changes in the contemporary design approaches to small house layouts which have evolved from a need for minimized space usage and a requirement for diverse living spatiality. Subsequently, thirty houses have been chosen to be analysed for the purpose of this study to reveal the differences between integrated and segregated spatial organizations in regard to flexibility, adaptability, transformability and permeability within the spaces. In addition to this, the new spatial relations will be overviewed considering spatial depth, interpenetration and density to define more implicit organizations which are able to expand constantly and accommodate different functional spaces in one open space with the help of spatial identifiers. The main focus of this research study concentrates on the above mentioned dynamic forms of spatiality that change from being weak to strong, implicit to explicit and indistinct to clearly defined spaces. These forms are measured, analysed and basically compare by means of a space syntax application on the values of the space and convex maps of the thirty selected houses. In summary, the analysis and measurement of the spatial characteristics of contemporary small houses in this sphere include both theoretical and empirical components. Firstly, the study discusses the basic definitions of spatial relations and organizations. Secondly, the space syntax method was used to test and compare new spatial design approaches by means of the Mean Depth, Mean Integration, Basic Difference Factor and Space Link Ratio values mainly to clarify how the spatiality changes according to the size although the plan type stays the same as 1+1.

scholarly journals Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Francisco Díaz-Pascual ◽  
Martin Lempp ◽  
Kazuki Nosho ◽  
Hannah Jeckel ◽  
Jeanyoung K Jo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Spatial Organization ◽  
Interaction Strength ◽  
Growth Dynamics ◽  
Nitrogen Sources ◽  
Spatial Arrangement ◽  
Model Systems ◽  
Biofilm Growth ◽  
Carbon And Nitrogen ◽  
And Function

Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.

Three-Dimensional Reconstruction Using Stereo Pairs from Serial Thick Sections

1977 ◽  
Vol 35 ◽  
pp. 562-563
Author(s):  
Robert Glaeser ◽  
Thomas Bauer ◽  
David Grano
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Thin Sections ◽  
3 Dimensional ◽  
Transmission Electron ◽  
Freeze Dried ◽  
Dimensional Reconstruction ◽  
Stereo Imagery ◽  
Whole Mounts

In transmission electron microscopy, the 3-dimensional structure of an object is usually obtained in one of two ways. For objects which can be included in one specimen, as for example with elements included in freeze- dried whole mounts and examined with a high voltage microscope, stereo pairs can be obtained which exhibit the 3-D structure of the element. For objects which can not be included in one specimen, the 3-D shape is obtained by reconstruction from serial sections. However, without stereo imagery, only detail which remains constant within the thickness of the section can be used in the reconstruction; consequently, the choice is between a low resolution reconstruction using a few thick sections and a better resolution reconstruction using many thin sections, generally a tedious chore. This paper describes an approach to 3-D reconstruction which uses stereo images of serial thick sections to reconstruct an object including detail which changes within the depth of an individual thick section.

A Novel Reconstitution Method for Inducing the Formation of Regular 2-Dimensional Arrays of Membrane Proteins and Lipids

1988 ◽  
Vol 46 ◽  
pp. 152-153 ◽  
Author(s):  
A. Engel ◽  
A. Holzenburg ◽  
K. Stauffer ◽  
J. Rosenbusch ◽  
U. Aebi
Keyword(s):  
Membrane Proteins ◽  
Flow Rate ◽  
Lipid Membranes ◽  
Functional Characterization ◽  
Dimensional Structure ◽  
Electron Crystallography ◽  
Peltier Element ◽  
Protein Ratio ◽  
Precise Control ◽  
3 Dimensional

Reconstitution of solubilized and purified membrane proteins in the presence of phospholipids into vesicles allows their functions to be studied by simple bulk measurements (e.g. diffusion of differently sized solutes) or by conductance measurements after transformation into planar membranes. On the other hand, reconstitution into regular protein-lipid arrays, usually forming at a specific lipid-to-protein ratio, provides the basis for determining the 3-dimensional structure of membrane proteins employing the tools of electron crystallography.To refine reconstitution conditions for reproducibly inducing formation of large and highly ordered protein-lipid membranes that are suitable for both electron crystallography and patch clamping experiments aimed at their functional characterization, we built a flow-dialysis device that allows precise control of temperature and flow-rate (Fig. 1). The flow rate is generated by a peristaltic pump and can be adjusted from 1 to 500 ml/h. The dialysis buffer is brought to a preselected temperature during its travel through a meandering path before it enters the dialysis reservoir. A Z-80 based computer controls a Peltier element allowing the temperature profile to be programmed as function of time.

Structure and Interaction of Protamine by Dark Field Electron Microscopy

1976 ◽  
Vol 34 ◽  
pp. 160-161
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Electron Microscopy ◽  
Dark Field ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
3 Dimensional ◽  
Field Electron ◽  
Proposed Model ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Positively Charged

It has been shown for some time that it is possible to obtain images of small unstained proteins, with a resolution of approximately 5Å using dark field electron microscopy (1,2). Applying this technique, we have observed a uniformity in size and shape of the 2-dimensional images of pure specimens of fish protamines (salmon, herring (clupeine, Y-l) and rainbow trout (Salmo irideus)). On the basis of these images, a model for the 3-dimensional structure of the fish protamines has been proposed (2).The known amino acid sequences of fish protamines show stretches of positively charged arginines, separated by regions of neutral amino acids (3). The proposed model for protamine structure (2) consists of an irregular, right-handed helix with the segments of adjacent arginines forming the loops of the coil.

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